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<li class="navelem"><b>claragenomics</b></li><li class="navelem"><a class="el" href="structclaragenomics_1_1Overlap.html">Overlap</a></li>  </ul>
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<a href="#pub-attribs">Public Attributes</a> &#124;
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<div class="title">claragenomics::Overlap Struct Reference</div>  </div>
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<p><code>#include &lt;<a class="el" href="types_8hpp_source.html">types.hpp</a>&gt;</code></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-attribs"></a>
Public Attributes</h2></td></tr>
<tr class="memitem:af754af96a8466548c56529e73446968d"><td class="memItemLeft" align="right" valign="top"><a id="af754af96a8466548c56529e73446968d"></a>
read_id_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1Overlap.html#af754af96a8466548c56529e73446968d">query_read_id_</a></td></tr>
<tr class="memdesc:af754af96a8466548c56529e73446968d"><td class="mdescLeft">&#160;</td><td class="mdescRight">internal read ID for query <br /></td></tr>
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<tr class="memitem:af4affa838e00cf52c9caf7c54e588f1f"><td class="memItemLeft" align="right" valign="top"><a id="af4affa838e00cf52c9caf7c54e588f1f"></a>
read_id_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1Overlap.html#af4affa838e00cf52c9caf7c54e588f1f">target_read_id_</a></td></tr>
<tr class="memdesc:af4affa838e00cf52c9caf7c54e588f1f"><td class="mdescLeft">&#160;</td><td class="mdescRight">internal read ID for target <br /></td></tr>
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<tr class="memitem:a3e19bc7577a0fa204af17a151741515b"><td class="memItemLeft" align="right" valign="top"><a id="a3e19bc7577a0fa204af17a151741515b"></a>
position_in_read_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1Overlap.html#a3e19bc7577a0fa204af17a151741515b">query_start_position_in_read_</a></td></tr>
<tr class="memdesc:a3e19bc7577a0fa204af17a151741515b"><td class="mdescLeft">&#160;</td><td class="mdescRight">start position in the query <br /></td></tr>
<tr class="separator:a3e19bc7577a0fa204af17a151741515b"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a3eabcb5dc36e07f6350a656f67a667b4"><td class="memItemLeft" align="right" valign="top"><a id="a3eabcb5dc36e07f6350a656f67a667b4"></a>
position_in_read_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1Overlap.html#a3eabcb5dc36e07f6350a656f67a667b4">target_start_position_in_read_</a></td></tr>
<tr class="memdesc:a3eabcb5dc36e07f6350a656f67a667b4"><td class="mdescLeft">&#160;</td><td class="mdescRight">start position in the target <br /></td></tr>
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<tr class="memitem:ae3fd1b5ace7323acf7036b9ff61b7fcd"><td class="memItemLeft" align="right" valign="top"><a id="ae3fd1b5ace7323acf7036b9ff61b7fcd"></a>
position_in_read_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1Overlap.html#ae3fd1b5ace7323acf7036b9ff61b7fcd">query_end_position_in_read_</a></td></tr>
<tr class="memdesc:ae3fd1b5ace7323acf7036b9ff61b7fcd"><td class="mdescLeft">&#160;</td><td class="mdescRight">end position in the query <br /></td></tr>
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position_in_read_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1Overlap.html#ad31894816486f1ef0310d9ffcbc66941">target_end_position_in_read_</a></td></tr>
<tr class="memdesc:ad31894816486f1ef0310d9ffcbc66941"><td class="mdescLeft">&#160;</td><td class="mdescRight">end position in the target <br /></td></tr>
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std::string&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1Overlap.html#adc3670fcf4b21bb9ee0d0dbeeb2afee9">query_read_name_</a></td></tr>
<tr class="memdesc:adc3670fcf4b21bb9ee0d0dbeeb2afee9"><td class="mdescLeft">&#160;</td><td class="mdescRight">query read name (e.g from FASTA) <br /></td></tr>
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std::string&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1Overlap.html#a8716fddd020d927f09c1d032a3d105f9">target_read_name_</a></td></tr>
<tr class="memdesc:a8716fddd020d927f09c1d032a3d105f9"><td class="mdescLeft">&#160;</td><td class="mdescRight">target read name (e.g from FASTA) <br /></td></tr>
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RelativeStrand&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1Overlap.html#a0de28565cb2f7a7a9cbbaf6af7365cff">relative_strand</a></td></tr>
<tr class="memdesc:a0de28565cb2f7a7a9cbbaf6af7365cff"><td class="mdescLeft">&#160;</td><td class="mdescRight">Relative strand: Forward ("+") or Reverse("-") <br /></td></tr>
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std::uint32_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1Overlap.html#a86bb5319d791d45f102cc3b3bf84e397">num_residues_</a> = 0</td></tr>
<tr class="memdesc:a86bb5319d791d45f102cc3b3bf84e397"><td class="mdescLeft">&#160;</td><td class="mdescRight">Number of residues (e.g anchors) between the two reads. <br /></td></tr>
<tr class="separator:a86bb5319d791d45f102cc3b3bf84e397"><td class="memSeparator" colspan="2">&#160;</td></tr>
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std::uint32_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1Overlap.html#adcdd8368a85d44729621f9304eb234ee">query_length_</a> = 0</td></tr>
<tr class="memdesc:adcdd8368a85d44729621f9304eb234ee"><td class="mdescLeft">&#160;</td><td class="mdescRight">Length of query sequence. <br /></td></tr>
<tr class="separator:adcdd8368a85d44729621f9304eb234ee"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ade99956ed23ad7cb5af94c66993403cb"><td class="memItemLeft" align="right" valign="top"><a id="ade99956ed23ad7cb5af94c66993403cb"></a>
std::uint32_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1Overlap.html#ade99956ed23ad7cb5af94c66993403cb">target_length_</a> = 0</td></tr>
<tr class="memdesc:ade99956ed23ad7cb5af94c66993403cb"><td class="mdescLeft">&#160;</td><td class="mdescRight">Length of target sequence. <br /></td></tr>
<tr class="separator:ade99956ed23ad7cb5af94c66993403cb"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a7ec04efd92437288c01bdc202a3272fb"><td class="memItemLeft" align="right" valign="top"><a id="a7ec04efd92437288c01bdc202a3272fb"></a>
bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1Overlap.html#a7ec04efd92437288c01bdc202a3272fb">overlap_complete</a> = false</td></tr>
<tr class="memdesc:a7ec04efd92437288c01bdc202a3272fb"><td class="mdescLeft">&#160;</td><td class="mdescRight">Whether the overlap is considered valid by the generating overlapper. <br /></td></tr>
<tr class="separator:a7ec04efd92437288c01bdc202a3272fb"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p><a class="el" href="structclaragenomics_1_1Overlap.html">Overlap</a> - represents one overlap between two substrings</p>
<p><a class="el" href="structclaragenomics_1_1Overlap.html">Overlap</a> is a region of two strings which is considered to be the same underlying biological sequence. The overlapping region need not be identical across both substrings. </p>
</div><hr/>The documentation for this struct was generated from the following file:<ul>
<li>cudamapper/include/cudamapper/<a class="el" href="types_8hpp_source.html">types.hpp</a></li>
</ul>
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